See Through Render Layer
Use "Alpha over" instead of "Add" node

Assuming that you are in a situation with a bright light sources behind your object like in the example below:



The use of an Color Add Node would sum the pixel colors from the two render layers, while what you probably want is to override the pixel color information basing on which layer is in front of you.

In this and your case, as both the layer of my light and your exaust are almost white, we can't see the "adding" because the are both almost full white, so what exceed the full white (RGB=1,1,1) is being clamped to 1.



Here's an exampe with a light source whose strength is 0.1, The addition is more visible now.





I would suggest to use the Alpha over node instead, which put the second imput image imput upon the first imput image taking alpha channel in account.





Remember that the second imput socket of the Alpha over node is the images that will be put above the source image (which is connected from the firts imput socket). So in your case, the source image must be the Exaust, and the second the Ship.

From the Blender reference manual's page about Alpha over node:


  Use this node to layer images on top of one another. This node takes two images as input, combines them by a factor, and outputs the image. Connect the Background image to the top input, and the foreground image to the lower input.